General information for g16125.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium- and chloride-dependent GABA transporter 1.
Parent gene
- The parent gene g16125 is located on chr_4: 8249729..8252860 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g16125 | g16125.t1 | isoform | g16125.t1 | 8249729 | 8252860 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon1 | 8249729 | 8249821 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS1 | 8249729 | 8249821 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon2 | 8249931 | 8250098 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS2 | 8249931 | 8250098 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon3 | 8250253 | 8250701 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS3 | 8250253 | 8250701 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon4 | 8250758 | 8250882 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS4 | 8250758 | 8250882 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon5 | 8250948 | 8251186 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS5 | 8250948 | 8251186 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon6 | 8251246 | 8251378 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS6 | 8251246 | 8251378 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon7 | 8251864 | 8252167 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS7 | 8251864 | 8252167 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon8 | 8252230 | 8252364 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS8 | 8252230 | 8252364 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon9 | 8252471 | 8252502 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS9 | 8252471 | 8252502 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon10 | 8252595 | 8252704 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS10 | 8252595 | 8252704 |
| chr_4 | g16125 | g16125.t1 | exon | g16125.t1.exon11 | 8252762 | 8252860 |
| chr_4 | g16125 | g16125.t1 | cds | g16125.t1.CDS11 | 8252762 | 8252860 |
| chr_4 | g16125 | g16125.t1 | TSS | g16125.t1 | NA | NA |
| chr_4 | g16125 | g16125.t1 | TTS | g16125.t1 | NA | NA |
Sequences
>g16125.t1 Gene=g16125 Length=1887
ATGACGATTGATTCAGAAGATGTCGAACTGCGACATAAAAATGATGATGTAGAAACACAA
GGCACATCAGGCCAACAATCACAGTCAACCACAATAGCTATAAGAAACACAAAATCAGAT
GATGATCCACTATTACGTGGTACATGGGGTAGTAAATTGGACTTTATTTTATCCGTCGTT
GGTCTTGCCATAGGTCTTGGCAACGTGTGGCGATTTCCATATCTGTGTTATAAAAATGGA
GGTGGCGCATTTCTTATACCTTACTTCATTACTCTTATTCTTGCCGGTATTCCAATGTTT
TTTATGGAATTGGCGCTTGGTCAAATGTTGACAATTGGTGGTCTTGGAGTATTTAAAATA
GCGCCAATTTTTAAAGGAATTGGTTATGCAGCAGCTGTCATGTCATGTTGGATGAATGTC
TACTACATTGTCATTCTTGCATGGGCCATTTTCTATTTCTTTATGTCAATGCGAGCAAAG
CTTCCGTGGAGTACGTGTGACAATTTTTGGAATACATACACATGCGTCAATCCCTATTTG
AGGAAAGATATTTGCTTCGATCAACGTGTGCCCGGACAATTTTTAGCAAATGGTACAGCT
GTCGTCGCTAAAGTATGTACTCTTGGTGGCAAAAATGTCTCAGCATCTATCTTGACAGAT
CCTGTCAAAGAATTTTGGGAACGCCGAGCATTGATGATTTCATCAGGAATTGAGGAAATA
GGAAATGTTCGTTGGGAGTTAGCTGGAACTTTATTATTTGTGTGGATTCTTTGCTATTTT
TGTATTTGGAAAGGTGTCAGATGGACAGGAAAAGTTGTCTATTTCACTGCTCTTTTCCCT
TATGTTCTTTTAACAATTTTGCTTATCAGAGGAATAACACTGCCAGGTGCTATGGAAGGA
ATTCGCTTCTATGTCACACCAAATTTATCAAAACTTCGCGAATCTGAAGTATGGATTGAT
GCGGTTACACAAATTTTCTTCTCATACGGTCTCGGTTTGGGTACATTAATGGCTCTTGGA
AGTTATAATAAATTCAATAATAATGTTTATAAAGATGCAGTAATTGTATGCGCTGTTAAT
TCATCAACATCAATGTTTGCTGGTTTTGTCATTTTCTCTGTTGTTGGTTTCATGGCTCAT
GAACAACAAAAACCAGTATCAGAGGTTGCTGCTTCTGGTCCTGGTTTGGCATTTTTGGCA
TATCCATCGGCTGTGTTACAACTGCCTGGTGCTCCACTTTGGGCAACTTTGTTTTTCTTT
ATGCTGCTACTCATTGGTCTTGATTCACAGTTTTGTACAATGGAAGGTTTTATAACTGCA
ATGGTGGATGAATGGCCACATCTTTTACGTAAACGAAAGGAACTTTTTATTGCTGTTGTT
TGCATTTTAAGTTACTTTGTGGGTTTCACTTGTATAACACAAGGCGGAATGTACATGTTC
CAAATTCTCGATTCTTATGCCGTCAGTGGTTTCTGCTTGCTTTTCTTAATCTTCTTTGAA
TGTATTTCAATCTCATGGTGCTTCGGTATTCAACGATTTTATGATGGAATCAAAGATATG
ATTGGTTATTATCCAATGGGATGGTGGAAATTCTGCTGGTGTGTTTCAACACCTTTCATT
TGTGTGAGTGTCTTTATTTTCAACCTTGTACAATGGACTCCAATTAAATACTTGGATTAT
GAATTTCCATGGTGGGCACATGCTTTTGGTTGGTTCACTGCTTTAAGTTCAATGTTGTGC
ATTCCTGGATACGCTATTTGGCTTTGGCAGAAAACTCCTGGTGATGCAATCGATAAACTC
CGACAAATTGTAAGAATTGATGACGATGTGACGACACTAAGAGGAAAAATGCAAGTTTAT
GCAAAGAAACTCAGTGAGAAATTATAG
>g16125.t1 Gene=g16125 Length=628
MTIDSEDVELRHKNDDVETQGTSGQQSQSTTIAIRNTKSDDDPLLRGTWGSKLDFILSVV
GLAIGLGNVWRFPYLCYKNGGGAFLIPYFITLILAGIPMFFMELALGQMLTIGGLGVFKI
APIFKGIGYAAAVMSCWMNVYYIVILAWAIFYFFMSMRAKLPWSTCDNFWNTYTCVNPYL
RKDICFDQRVPGQFLANGTAVVAKVCTLGGKNVSASILTDPVKEFWERRALMISSGIEEI
GNVRWELAGTLLFVWILCYFCIWKGVRWTGKVVYFTALFPYVLLTILLIRGITLPGAMEG
IRFYVTPNLSKLRESEVWIDAVTQIFFSYGLGLGTLMALGSYNKFNNNVYKDAVIVCAVN
SSTSMFAGFVIFSVVGFMAHEQQKPVSEVAASGPGLAFLAYPSAVLQLPGAPLWATLFFF
MLLLIGLDSQFCTMEGFITAMVDEWPHLLRKRKELFIAVVCILSYFVGFTCITQGGMYMF
QILDSYAVSGFCLLFLIFFECISISWCFGIQRFYDGIKDMIGYYPMGWWKFCWCVSTPFI
CVSVFIFNLVQWTPIKYLDYEFPWWAHAFGWFTALSSMLCIPGYAIWLWQKTPGDAIDKL
RQIVRIDDDVTTLRGKMQVYAKKLSEKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 42 | g16125.t1 | CDD | cd11496 | SLC6sbd-TauT-like | 46 | 606 | 0.0 |
| 58 | g16125.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 33 | - |
| 59 | g16125.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 57 | g16125.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 19 | 33 | - |
| 2 | g16125.t1 | PANTHER | PTHR11616:SF104 | TRANSPORTER | 42 | 183 | 6.0E-243 |
| 4 | g16125.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 42 | 183 | 6.0E-243 |
| 3 | g16125.t1 | PANTHER | PTHR11616:SF104 | TRANSPORTER | 216 | 614 | 6.0E-243 |
| 5 | g16125.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 216 | 614 | 6.0E-243 |
| 9 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 54 | 75 | 4.8E-84 |
| 11 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 83 | 102 | 4.8E-84 |
| 12 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 126 | 152 | 4.8E-84 |
| 7 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 272 | 289 | 4.8E-84 |
| 10 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 354 | 374 | 4.8E-84 |
| 8 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 408 | 427 | 4.8E-84 |
| 6 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 490 | 510 | 4.8E-84 |
| 13 | g16125.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 530 | 550 | 4.8E-84 |
| 1 | g16125.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 46 | 589 | 3.5E-220 |
| 23 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 54 | - |
| 32 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 72 | - |
| 19 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 73 | 83 | - |
| 38 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 106 | - |
| 25 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 107 | 125 | - |
| 40 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 154 | - |
| 16 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 155 | 246 | - |
| 30 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 266 | - |
| 28 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 267 | 271 | - |
| 39 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 296 | - |
| 21 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 297 | 316 | - |
| 37 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 317 | 341 | - |
| 26 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 342 | 352 | - |
| 34 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 353 | 377 | - |
| 18 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 378 | 388 | - |
| 35 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 389 | 408 | - |
| 22 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 409 | 413 | - |
| 41 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 414 | 434 | - |
| 15 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 435 | 454 | - |
| 31 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 455 | 480 | - |
| 27 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 481 | 485 | - |
| 36 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 486 | 510 | - |
| 17 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 511 | 530 | - |
| 33 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 531 | 552 | - |
| 24 | g16125.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 553 | 563 | - |
| 29 | g16125.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 564 | 589 | - |
| 20 | g16125.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 590 | 628 | - |
| 56 | g16125.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 70 | 84 | - |
| 60 | g16125.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 45 | 594 | 109.299 |
| 14 | g16125.t1 | SUPERFAMILY | SSF161070 | SNF-like | 46 | 590 | 1.26E-178 |
| 47 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 72 | - |
| 50 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 101 | - |
| 45 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 111 | 133 | - |
| 52 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 140 | 159 | - |
| 53 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 241 | 263 | - |
| 49 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 294 | - |
| 54 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 321 | 343 | - |
| 55 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 356 | 378 | - |
| 48 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 405 | 427 | - |
| 44 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 455 | 477 | - |
| 43 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 487 | 509 | - |
| 46 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 530 | 552 | - |
| 51 | g16125.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 567 | 589 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K05034 (solute carrier family 6 (neurotransmitter transporter, GABA) member 1)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed